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There's an extra HTTP request to fetch the manifest on every page load.

In the same vein, does the browser check if files specified in the manifest expired? If yes it would once again waste some time...

But it will be eventually be written in JavaScript.

Doesn't the using the application cache (e.g. the manifest file you speak of) cause a user prompt? That's a deal breaker in many situations.

I am using a manifest in my new app and never witnessed a user prompt. I am testing on Android 2.2 native browser, chrome and safari.

It is my understanding that desktop browsers do present the prompt, but mobile browsers do not. This feature was mostly designed for mobile, since the browser cache in mobile tends to be constrained. I have a feeling as things move along, that prompt will go away entirely.